# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 04:47:50 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 2-amino-9-[2-(3-carboxy-4-hydroxyphenyl)-2-oxoethyl]-7-methyl-6-oxo-6,7-dihydro-1H-purin-9-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c[n+](CC(=O)c2ccc(O)c(c2)C(O)=O)c3N=C(N)NC(=O)c13
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 41G  41G  2-amino-9-[2-(3-carboxy-4-hydroxyphenyl)-2-oxoethyl]-7-methyl-6-oxo-6,7-dihydro-1H-purin-9-ium  ligand  39  25  .  2021-08-04  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_41G
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 41G  N1    N  NR16  0  -0.733   4.4793   1.7062  -0.1990
 41G  C2    C  CR6   0   0.727   3.3182   2.1169   0.3952
 41G  N2    N  NH2   0  -0.823   3.1851   3.4131   0.6426
 41G  N3    N  N     0  -0.503   2.3522   1.2835   0.7263
 41G  C4    C  CR56  0   0.519   2.6250   0.0209   0.4251
 41G  C5    C  CR56  0   0.089   3.7549  -0.4832  -0.1711
 41G  C6    C  CR6   0   0.563   4.8164   0.3960  -0.5401
 41G  O6    O  O     0  -0.441   5.8735   0.1225  -1.0705
 41G  N7    N  NR5   0  -0.466   3.5856  -1.8455  -0.2930
 41G  C8    C  CR15  0   0.262   2.4103  -2.1516   0.2063
 41G  N9    N  NR5   1  -0.497   1.8059  -1.0505   0.6674
 41G  CG    C  CR6   0  -0.013  -1.9117  -0.3624   0.4568
 41G  ON2   O  OH1   0  -0.577  -4.6171   0.7298  -2.4704
 41G  CZ    C  CR6   0   0.394  -4.6181   0.0222   1.0934
 41G  C1'   C  CH2   0  -0.458   0.4658  -0.9683   1.1868
 41G  C2'   C  C     0   0.365  -0.5027  -0.5607   0.0823
 41G  O2'   O  O     0  -0.377  -0.0961  -0.4222  -1.0484
 41G  CD1   C  CR16  0  -0.265  -2.3770  -0.5345   1.7684
 41G  ON    O  O     0  -0.478  -6.3154   0.7738  -1.0323
 41G  CD2   C  CR16  0  -0.272  -2.8209   0.0042  -0.5265
 41G  CE1   C  CR16  0  -0.321  -3.7012  -0.3477   2.0837
 41G  CE2   C  CR6   0  -0.211  -4.1645   0.2013  -0.2328
 41G  CM7   C  CH3   0  -0.523   4.5397  -2.7875  -0.8548
 41G  H1    H  HNR6  0   0.440   5.1761   2.4062  -0.4253
 41G  H21N  H  HNH2  0   0.429   3.8736   4.0921   0.3667
 41G  H22N  H  HNH2  0   0.426   2.3281   3.7490   1.0480
 41G  HM71  H  HCH3  0   0.286   5.4481  -2.7842  -0.2597
 41G  HM72  H  HCH3  0   0.283   4.0985  -3.7785  -0.8388
 41G  HM73  H  HCH3  0   0.286   4.7674  -2.5067  -1.8782
 41G  H8    H  HCR5  0   0.373   1.9968  -3.1457   0.2546
 41G  H1'1  H  HCH2  0   0.342   0.1872  -1.9383   1.6003
 41G  H1'2  H  HCH2  0   0.331   0.4523  -0.2497   2.0070
 41G  HD2   H  HCR6  0   0.284  -2.4692   0.1378  -1.5405
 41G  HD1   H  HCR6  0   0.280  -1.7046  -0.8174   2.5678
 41G  HN2   H  HOH1  0   0.498  -5.3028   0.9831  -3.1074
 41G  HE1   H  HCR6  0   0.288  -4.0486  -0.4827   3.0993
 41G  HH    H  HOH1  0   0.486  -6.3998   0.4466   0.6596
 41G  OH    O  OH1   0  -0.602  -5.8790   0.1885   1.4519
 41G  CN    C  C     0   0.607  -5.1328   0.5927  -1.2692

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 41G  O6   C6    double    1.214  0.020  1.214
 41G  C6   N1    single    1.395  0.020  1.395
 41G  C6   C5    single    1.427  0.020  1.427
 41G  N1   C2    single    1.367  0.020  1.367
 41G  C2   N2    single    1.326  0.020  1.326
 41G  C2   N3    double    1.318  0.020  1.318
 41G  N3   C4    single    1.326  0.020  1.326
 41G  C5   C4    aromatic  1.373  0.020  1.373
 41G  C5   N7    aromatic  1.378  0.020  1.378
 41G  C4   N9    aromatic  1.370  0.020  1.370
 41G  N7   CM7   single    1.454  0.020  1.454
 41G  N7   C8    aromatic  1.313  0.020  1.313
 41G  C8   N9    aromatic  1.338  0.020  1.338
 41G  N9   C1'   single    1.440  0.020  1.440
 41G  C1'  C2'   single    1.524  0.020  1.524
 41G  C2'  O2'   double    1.210  0.020  1.210
 41G  C2'  CG    single    1.471  0.020  1.471
 41G  CG   CD2   aromatic  1.388  0.020  1.388
 41G  CG   CD1   aromatic  1.402  0.020  1.402
 41G  CD2  CE2   aromatic  1.389  0.020  1.389
 41G  CE2  CN    single    1.471  0.020  1.471
 41G  CE2  CZ    aromatic  1.413  0.020  1.413
 41G  CN   ON2   single    1.314  0.020  1.314
 41G  CN   ON    double    1.220  0.020  1.220
 41G  CD1  CE1   aromatic  1.374  0.020  1.374
 41G  CE1  CZ    aromatic  1.399  0.020  1.399
 41G  CZ   OH    single    1.321  0.020  1.321
 41G  N1   H1    single    0.860  0.020  1.020
 41G  N2   H21N  single    0.860  0.020  1.020
 41G  N2   H22N  single    0.860  0.020  1.020
 41G  CM7  HM71  single    0.970  0.020  1.090
 41G  CM7  HM72  single    0.970  0.020  1.090
 41G  CM7  HM73  single    0.970  0.020  1.090
 41G  C8   H8    single    0.930  0.020  1.080
 41G  C1'  H1'1  single    0.970  0.020  1.090
 41G  C1'  H1'2  single    0.970  0.020  1.090
 41G  CD2  HD2   single    0.930  0.020  1.080
 41G  CD1  HD1   single    0.930  0.020  1.080
 41G  ON2  HN2   single    0.850  0.020  0.980
 41G  CE1  HE1   single    0.930  0.020  1.080
 41G  OH   HH    single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 41G  H1    N1   C6    115.34  3.000
 41G  H1    N1   C2    118.26  3.000
 41G  C6    N1   C2    126.40  3.000
 41G  N3    C2   N2    119.84  3.000
 41G  N3    C2   N1    122.79  3.000
 41G  N2    C2   N1    117.38  3.000
 41G  H22N  N2   H21N  117.93  3.000
 41G  H22N  N2   C2    119.15  3.000
 41G  H21N  N2   C2    122.68  3.000
 41G  C4    N3   C2    113.21  3.000
 41G  N9    C4   C5    106.35  3.000
 41G  N9    C4   N3    125.53  3.000
 41G  C5    C4   N3    128.11  3.000
 41G  N7    C5   C6    132.66  3.000
 41G  N7    C5   C4    107.47  3.000
 41G  C6    C5   C4    119.88  3.000
 41G  O6    C6   C5    128.47  3.000
 41G  C5    C6   N1    109.61  3.000
 41G  O6    C6   N1    121.92  3.000
 41G  CM7   N7   C8    125.68  3.000
 41G  C8    N7   C5    107.87  3.000
 41G  CM7   N7   C5    126.45  3.000
 41G  H8    C8   N9    124.77  3.000
 41G  H8    C8   N7    125.13  3.000
 41G  N9    C8   N7    110.09  3.000
 41G  C1'   N9   C8    126.29  3.000
 41G  C1'   N9   C4    125.14  3.000
 41G  C8    N9   C4    108.21  3.000
 41G  CD2   CG   CD1   118.53  3.000
 41G  CD1   CG   C2'   122.63  3.000
 41G  CD2   CG   C2'   118.84  3.000
 41G  HN2   ON2  CN    110.50  3.000
 41G  CE2   CZ   CE1   119.17  3.000
 41G  CE1   CZ   OH    117.81  3.000
 41G  CE2   CZ   OH    123.02  3.000
 41G  H1'2  C1'  H1'1  107.32  3.000
 41G  H1'2  C1'  C2'   111.15  3.000
 41G  H1'1  C1'  C2'   110.50  3.000
 41G  H1'2  C1'  N9    108.70  3.000
 41G  H1'1  C1'  N9    108.89  3.000
 41G  C2'   C1'  N9    110.20  3.000
 41G  O2'   C2'  C1'   119.63  3.000
 41G  O2'   C2'  CG    122.98  3.000
 41G  C1'   C2'  CG    117.39  3.000
 41G  HD1   CD1  CE1   117.70  3.000
 41G  HD1   CD1  CG    121.12  3.000
 41G  CE1   CD1  CG    121.18  3.000
 41G  HD2   CD2  CE2   119.67  3.000
 41G  HD2   CD2  CG    118.93  3.000
 41G  CE2   CD2  CG    121.40  3.000
 41G  HE1   CE1  CD1   120.53  3.000
 41G  HE1   CE1  CZ    119.14  3.000
 41G  CD1   CE1  CZ    120.33  3.000
 41G  CD2   CE2  CZ    119.39  3.000
 41G  CZ    CE2  CN    118.92  3.000
 41G  CD2   CE2  CN    121.69  3.000
 41G  HM73  CM7  HM72  109.60  3.000
 41G  HM73  CM7  HM71  109.90  3.000
 41G  HM72  CM7  HM71  109.57  3.000
 41G  HM73  CM7  N7    109.54  3.000
 41G  HM72  CM7  N7    108.62  3.000
 41G  HM71  CM7  N7    109.59  3.000
 41G  HH    OH   CZ    108.66  3.000
 41G  CE2   CN   ON    122.74  3.000
 41G  ON    CN   ON2   122.85  3.000
 41G  CE2   CN   ON2   114.42  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 41G  CONST_01  C8    N7   C5   C4      0.00   0.0  0
 41G  CONST_02  N7    C8   N9   C4      0.00   0.0  0
 41G  CONST_03  C8    N9   C4   C5      0.00   0.0  0
 41G  CONST_04  N9    C8   N7   C5      0.00   0.0  0
 41G  CONST_05  N9    C4   C5   N7      0.00   0.0  0
 41G  CONST_06  CZ    CE2  CD2  CG      0.00   0.0  0
 41G  CONST_07  CZ    CE1  CD1  CG      0.00   0.0  0
 41G  CONST_08  CE2   CD2  CG   CD1     0.00   0.0  0
 41G  CONST_09  CE2   CZ   CE1  CD1     0.00   0.0  0
 41G  CONST_10  CE1   CD1  CG   CD2     0.00   0.0  0
 41G  CONST_11  CE1   CZ   CE2  CD2     0.00   0.0  0
 41G  CONST_12  C4    N3   C2   N1      0.00   0.0  0
 41G  CONST_13  C5    C6   N1   C2      0.00   0.0  0
 41G  CONST_14  C6    N1   C2   N3      0.00   0.0  0
 41G  CONST_15  C1'   N9   C4   N3      0.00   0.0  0
 41G  CONST_16  CM7   N7   C5   C4    180.00   0.0  0
 41G  CONST_17  C1'   N9   C4   C5    180.00   0.0  0
 41G  CONST_18  CM7   N7   C5   C6      0.00   0.0  0
 41G  CONST_19  C1'   N9   C8   N7    180.00   0.0  0
 41G  CONST_20  CM7   N7   C8   N9    180.00   0.0  0
 41G  CONST_21  CN    CE2  CD2  CG    180.00   0.0  0
 41G  CONST_22  CD2   CE2  CZ   OH    180.00   0.0  0
 41G  CONST_23  CD1   CE1  CZ   OH    180.00   0.0  0
 41G  CONST_24  CE1   CZ   CE2  CN    180.00   0.0  0
 41G  CONST_25  CE2   CD2  CG   C2'   180.00   0.0  0
 41G  CONST_26  CE1   CD1  CG   C2'   180.00   0.0  0
 41G  CONST_27  O6    C6   N1   C2    180.00   0.0  0
 41G  CONST_28  C6    N1   C2   N2    180.00   0.0  0
 41G  CONST_29  C4    N3   C2   N2    180.00   0.0  0
 41G  CONST_30  H8    C8   N9   C4    180.00   0.0  0
 41G  CONST_31  HE1   CE1  CD1  CG    180.00   0.0  0
 41G  CONST_32  HD2   CD2  CE2  CZ    180.00   0.0  0
 41G  CONST_33  HD1   CD1  CE1  CZ    180.00   0.0  0
 41G  CONST_34  H1    N1   C2   N3    180.00   0.0  0
 41G  CONST_35  H21N  N2   C2   N1      0.00   0.0  0
 41G  CONST_36  H22N  N2   C2   N1    180.00   0.0  0
 41G  CONST_37  HN2   ON2  CN   CE2   180.00   0.0  0
 41G  Var_01    C2'   C1'  N9   C4     78.26  30.0  2
 41G  Var_02    CG    C2'  C1'  N9   -176.98  30.0  3
 41G  Var_03    CD2   CE2  CN   ON2     0.22  30.0  2
 41G  Var_04    CD2   CG   C2'  C1'  -179.76  30.0  2
 41G  Var_05    HM71  CM7  N7   C5     62.20  30.0  2

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 41G  plan-1  CG    0.020
 41G  plan-1  CZ    0.020
 41G  plan-1  C2'   0.020
 41G  plan-1  CD1   0.020
 41G  plan-1  CD2   0.020
 41G  plan-1  CE1   0.020
 41G  plan-1  CE2   0.020
 41G  plan-1  HD2   0.020
 41G  plan-1  HD1   0.020
 41G  plan-1  HE1   0.020
 41G  plan-1  OH    0.020
 41G  plan-1  CN    0.020
 41G  plan-2  N1    0.020
 41G  plan-2  C2    0.020
 41G  plan-2  N2    0.020
 41G  plan-2  N3    0.020
 41G  plan-2  C4    0.020
 41G  plan-2  C5    0.020
 41G  plan-2  C6    0.020
 41G  plan-2  O6    0.020
 41G  plan-2  N7    0.020
 41G  plan-2  C8    0.020
 41G  plan-2  N9    0.020
 41G  plan-2  C1'   0.020
 41G  plan-2  CM7   0.020
 41G  plan-2  H1    0.020
 41G  plan-2  H21N  0.020
 41G  plan-2  H22N  0.020
 41G  plan-2  H8    0.020
 41G  plan-3  CG    0.020
 41G  plan-3  C1'   0.020
 41G  plan-3  C2'   0.020
 41G  plan-3  O2'   0.020
 41G  plan-4  ON2   0.020
 41G  plan-4  ON    0.020
 41G  plan-4  CE2   0.020
 41G  plan-4  HN2   0.020
 41G  plan-4  CN    0.020

